One of the most influential findings of the last 20 years in molecular evolutionary studies has been that recombination rate is frequently correlated with nucleotide sequence diversity within a species. In Drosophila species, this relationship has been attributed to natural selection, while neutral causes have been attributed as primary contributors to this association in humans. However, the relationship of recombination to diversity has not been observed in all species examined, and conflicting reports also exist on whether recombination rate is associated with interspecies sequence divergence or codon usage bias. If there is fine-scale heterogeneity in recombination rate across a genome, the conflicting conclusions could result from differences in the scale with which recombination is measured. Additionally, interpreting the evolutionary causes of these associations to recombination rate can be facilitated by evaluations at multiple scales. This proposal takes a collaborative and interdisciplinary approach to tackling these oft- cited relationships. Building upon a successful preliminary study, the investigators will construct very high resolution linkage maps using the species Drosophila pseudoobscura, and correlate local recombination rates to various sequence motifs. They will also generate multiple whole-genome sequence assemblies of this species from which to carefully examine patterns of nucleotide diversity at an unprecedented scale. Finally, extensive modeling is proposed to examine possible effects of background selection and selective sweeps to infer conditions under which they can operate to produce the observed associations between recombination rate and diversity, divergence, or codon bias. The investigators have extensive experience with all of the proposed work, as illustrated by the preliminary results reported. PUBLIC HEALTH RELEVANCE: Drosophila fruit flies and humans likely share many metabolic housekeeping genes and thus could experience similar absolute selection coefficients. Because humans have a much smaller population size, we accumulate many detrimental mutations that would be eliminated in Drosophila, so quantifying the contributions of such classes of mutations to genome evolution using a model system could potentially inform the rate of accumulation of hereditary human diseases.